In 1963, he began working on an arms control proposal for preventing anti-ballistic missile (ABM) systems.[6] In 1964-1966 he was a research associate at the Harvard Center for International Affairs (CFIA) where he wrote two books: Containing the Arms Race: Some Specific Proposals (MIT Press, 1966) and Strategic Persuasion: Arms Control Through Dialogue (Columbia University Press, 1967). He taught mathematics and arms control at Pomona College from 1966-68.

During the 30 years of Stone's stewardship, he and the Federation contributed to policy debates on the nuclear arms race, human rights, ethnic violence and civil conflict, small arms, controlling biological and chemical weapons, energy conservation, global warming, and related subjects.

Several of Stone's arms control initiatives bore fruit. According to the 2002 book Unarmed Forces by Matthew Evangelista, the Russians were calling the ABM Treaty "Jeremy Stone's proposal" as early as 1967.[7] Stone designed and secured Carter Administration approval of a follow-on to SALT II ("Shrink SALT II") which was proposed in secret by President Carter at the 1979 Vienna Summit.[8] He invented a finesse (the Bear Hug Strategy) that may have helped to make START II possible.[9] And he created an entirely new approach ("No One Decision-Maker") to the issue of no-first-use of nuclear weapons.[10]

In the 1970s, Stone and FAS helped catalyze the opening of scientific exchange with China in 1972.[11] He persuaded the American scientific community to set up human rights committees to defend the rights of Russian scientists[12] and was a leading American advocate for SovietphysicistAndrei Sakharov, who in 1976 described Stone as "creative, articulate and brave."[13]

He was instrumental in stopping an illegal U.S. Government program of mail opening by the CIA.[14] He is credited with having made major contributions to changing U.S. policy on Cambodia at a time when that policy had allied the United States to the genocidal Khmer Rouge.[15] He also waged an effective campaign to have the CIA and the KGB work together on issues of common concern.[16] And he once was assigned, by Carl Sagan, the difficult task of determining whether to warn the East Coast of the United States of a possible impending earthquake.[17]

In April 1999, Public Affairs Press published his memoir, "Every Man Should Try": Adventures of a Public Interest Activist, in which he documented his achievements and failures–including those noted above. (The book was published in Russian in March 2004 with an introduction by Academician Evgeny Velikhov.)

In December 1998, he led the first American scientific delegation in 20 years to Iran and, in September 1999, hosted the return visit of the Academy of Sciences of Iran. Introducing this delegation to a host of scientific organizations in Washington, including the National Academy of Sciences, led to an agreement to restart the (post-1979 revolution) Iranian-American scientific exchange.[18]

Stone published his second memoir, "Catalytic Diplomacy: Russia, China, North Korea, and Iran," in October 2009.[19] Available on Amazon.com, it covers his work from 1999 to 2006. It can be printed out from his foreign policy website www.catalyticdiplomacy.org as can his first life memoir.

A 100 page summary of his main achievements on foreign affairs for the half-century from 1962 to 2014 also appears on the Catalytic Diplomacy website under the tab "Life Memoirs Summary".

After resigning from the Presidency of the Federation of American Scientists on June 1, 2000, he formed the small non-profit, Catalytic Diplomacy,[20] which from 1999 to 2006 worked mainly on Cross-Straits Relations between China and Taiwan; U.S.-Russian arms control; U.S. relations with Iran; and U.S. relations with North Korea. Beginning in 2007, working with a small group of activists, he has been working on issues involving Myanmar (Burma), Cuba, and Afghanistan and Iran.

In 2010, Stone created an organization, Catalytic Longevity,[22] to advance a dietary approach called "Carbohydrate Concentration." This website is powered by the work of its research director, Mark McCarty, and a few others and is, as of 2015, working on treating neurological disorders by nutritional means, especially with ketogenic diets and coconut oil.

In 2014, he reported on his work on religion on a website at www.catalyticreligion.org. This website documents the fact that the main architects of the three largest Western religions—Christianity (Apostle Paul), Islam (Mohammad) and Protestantism (Martin Luther)--all suffered from the same mental disorder, a disorder that encourages the creation of new religion. The disorder is epilepsy/Geschwind's Syndrome.

In 2015, Catalytic Diplomacy reported on its work on Journalistic Independence and Peace by posting two videos on the www.ifstone.org website describing the career of Jeremy Stone’s father, I.F. Stone, and journalists who followed his example. These videos are the precursor of a 90-minute documentary being created by White Pine Pictures of Toronto, Canada.

Stone has received the Science and Society Award of the Forum on Physics and Society of the American Physics Society. In June 1985, he was awarded an honorary Doctor of Laws degree from Swarthmore College. And, in 1995, the Federation of American Scientists gave Stone its annual Public Service Award.[23]

The Stanford-based professor and hero of Michael Crichton's 1969 novel and movie The Andromeda Strain is named "Dr. Jeremy Stone." Dr. Stone himself was in Stanford in 1969 but unlike the fictional character was studying post-graduate economics, not biology. There is also a comic strip hero with the name Dr. Jeremy Stone, whose alter ego is the superbly muscled Maul.

^"Every Man Should Try", Chapter 20 ("Should SALT II Be Ratified and What Form Should SALT III Take?"); and Jimmy Carter, Keeping Faith: Memoirs of a President (University of Arkansas Press, 1995), pp. 248 and 251,

^"Every Man Should Try", chapters 14-16 (Defending Sakharov Through NAS and Moscow; Defense of Sakharov via Dobrynin and the Media; Would Moscow Give Sakharov to Kennedy?); the Sakharov quotation is at p. 152